docs: def nucmer_hits_to_ref_and_qry_coords(cls, nucmer_hits, contig=None):
          '''Same as nucmer_hits_to_ref_coords, except removes containing hits first,
             and returns ref and qry coords lists'''
          if contig is None:
              ctg_coords = {key: [] for key in nucmer_hits.keys()}
          else:
              ctg_coords = {contig: []}
  
          ref_coords = {}
  
          for key in ctg_coords:
              hits = copy.copy(nucmer_hits[key])
              hits.sort(key=lambda x: len(x.ref_coords()))
  
              if len(hits) > 1:
                  i = 0
                  while i < len(hits) - 1:
                      c1 = hits[i].ref_coords()
                      c2 = hits[i+1].ref_coords()
                      if c2.contains(c1):
                          hits.pop(i)
                      else:
                          i += 1
  
              ref_coords[key] = [hit.ref_coords() for hit in hits]
              ctg_coords[key] = [hit.qry_coords() for hit in hits]
              pyfastaq.intervals.merge_overlapping_in_list(ref_coords[key])
              pyfastaq.intervals.merge_overlapping_in_list(ctg_coords[key])
  
          return ctg_coords, ref_coords